Shotgun proteomics

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Proteomics (22127)
Unknown (1132)
Transcriptomics (129)
Genomics (74)
Metabolomics (23)
Other (22)
Multiomics (6)

Organisms

Homo sapiens (161)
Mus musculus (45)
Escherichia coli (12)
Saccharomyces cerevisiae (5)
Burkholderia cenocepacia H111 (4)
Bacteria (3)
Caenorhabditis elegans (3)
Rattus norvegicus (3)
Drosophila melanogaster (3)
Chlamydomonas reinhardtii (2)
Solanum tuberosum (2)
Burkholderia cenocepacia (2)
Danio rerio (2)
Bacteroides cellulosilyticus (2)
Dorea longicatena DSM 13814 (2)
Bartonella henselae (2)
Streptomyces coelicolor (2)
Triticum aestivum (2)
Larimichthys crocea (1)
Shewanella oneidensis MR-1 (1)
Bombyx mori (1)
Streptococcus thermophilus (1)
Bacillus thuringiensis (1)
Neospora caninum (1)
Schizosaccharomyces pombe 972h- (1)
Toxoplasma gondii (1)
Xenopus laevis (1)
Solanum lycopersicum (1)
Glycine max (1)
Escherichia coli str. K-12 substr. MG1655 (1)

Organisms

Homo sapiens (15)
Mus musculus (6)
Caenorhabditis elegans (3)
Burkholderia cenocepacia H111 (2)
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (2)
Legionella pneumophila str. Paris (1)
Ophrys (1)
Lactiplantibacillus plantarum WCFS1 (1)
Spirodela polyrhiza (1)
Caballeronia glathei (1)
Haliotis rufescens (1)
Toxoplasma gondii VEG (1)
572307 (1)
Streptomyces coelicolor (1)
Erythranthe guttata (1)
Bartonella henselae (1)
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (1)
Schmidtea mediterranea (1)
Bacteria (1)
Bacillus subtilis subsp. subtilis str. 168 (1)
Arabidopsis thaliana (1)

Repository

pride (21590)
MassIVE (306)
biostudies-arrayexpress (111)
jPOST (61)
ENA (59)
iProX (53)
PAXDB (49)
PeptideAtlas (47)
geo (32)
GPMDB (19)
PanoramaPublic (17)
MetaboLights (15)
GNPS (8)
EGA (3)
LINCS (3)
ExpressionAtlas (1)
NODE (1)

Tissue

Cell culture (4273)
Epithelial cell (1291)
Brain (1228)
Liver (719)
Permanent cell line cell (668)
Plant cell (604)
Blood plasma (553)
Leaf (546)
Blood (488)
Kidney (453)
Heart (440)
Fibroblast (437)
Lung (416)
Whole body (404)
Cell suspension culture (340)
T cell (327)
Colon (299)
Macrophage (293)
Blood cell (287)
Blood serum (281)
Root (248)
Hepatocyte (244)
B cell (243)
Skin (243)
Stem cell (217)
Embryo (205)
Others (32)
Brain (1)
Breast (1)
Urine (1)

Disease

Disease free (534)
Breast cancer (490)
Colon cancer (303)
Acute leukemia (231)
Cardiovascular system disease (146)
Alzheimer's disease (144)
Cervix carcinoma (144)
Malignant neoplasm of ovary (118)
Melanoma (100)
Wounds and Injuries (100)
Parkinson's disease (92)
Prostate adenocarcinoma (89)
Brain cancer (86)
Lymphoma (79)
Type 2 diabetes mellitus (79)
COVID-19 (73)
Lung cancer (71)
Glioblastoma (63)
Brain glioblastoma multiforme (59)
Non-small cell lung carcinoma (59)
Neuroblastoma (58)
Amyotrophic lateral sclerosis (49)
Hepatocellular carcinoma (48)
Plasmodium falciparum malaria (44)
Influenza (41)
Pancreatic cancer (40)
Pancreatic ductal adenocarcinoma (40)
Tuberculosis (40)
Severe acute respiratory syndrome (38)
Not Available (19)

Technology Type

Mass Spectrometry (21590)
Shotgun proteomics (21068)
Affinity purification coupled with mass spectrometry proteomics (1162)
Gel-based experiment (710)
SWATH MS (386)
Bottom-up proteomics (343)
SRM/MRM (197)
Data-dependent acquisition (163)
Top-down proteomics (146)
Chemical cross-linking coupled with mass spectrometry proteomics (116)
HDMSE (94)
All-ion fragmentation (58)
Data-independent acquisition (37)
MSE (29)
Mass spectrometry imaging (20)
Mass spectrometry (13)
Affinity proteomics (4)
Mass spectrometry (3)
Shotgun-MS (3)
Metaproteomics (3)
PAcIFIC (3)
Mass spectrometry assay (2)
Proteogenomics (2)
RNA mass spectrometry (2)
DiaPASEF (1)
Gel-free quantification method (1)
Glycoproteomics (1)
Immunopeptidomics (1)
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (1)

Instrument Platform

Q Exactive (80)
LTQ Orbitrap Velos (42)
LTQ Orbitrap Elite (20)
Instrument (19)
LTQ (19)
Q Exactive HF (18)
Orbitrap Fusion (17)
Orbitrap Fusion Lumos (17)
LTQ Orbitrap (13)
Q Exactive Plus (13)
TimsTOF Pro (12)
Illumina HiSeq 2500 (11)
Illumina HiSeq 2000 (10)
NextSeq 500 (8)
Orbitrap Eclipse (7)
TSQ Quantiva (7)
Illumina NovaSeq 6000 (6)
Impact II (6)
LTQ XL (5)
Illumina Genome Analyzer II (3)
Illumina HiSeq 4000 (3)
MGISEQ-2000RS (1)
GenePix 4000 (1)
Affymetrix Gene Atlas System (1)
Agilent 2100 Bioanalyzer (1)
Illumina HiSeq X (1)
NextSeq 550 (1)
Illumina HiSeq 3000 (1)
6495C Triple Quadrupole LC/MS (1)
Q-Exactive Orbitrap (1)

Publication Date

2022 (3660)
2023 (3333)
2021 (3049)
2020 (2252)
2024 (1983)
2019 (1955)
2018 (1693)
2017 (1085)
2016 (977)
2025 (926)
2015 (594)
2014 (309)
2026 (255)
2013 (70)
2011 (25)
2010 (25)
2012 (21)
2008 (9)
2006 (7)
2009 (5)
2007 (1)

UNIPROT ID/AC

2AAA_MOUSE (10)
3HIDH_MOUSE (10)
6PGL_MOUSE (10)
AATC_MOUSE (10)
AATM_MOUSE (10)
ACBP_MOUSE (10)
ACINU_MOUSE (10)
ACL6A_MOUSE (10)
ACON_MOUSE (10)
ACTN4_MOUSE (10)
ADK_MOUSE (10)
AHSA1_MOUSE (10)
ALDH2_MOUSE (10)
ALDOA_MOUSE (10)
ALDR_MOUSE (10)
AMPL_MOUSE (10)
AMRP_MOUSE (10)
ANXA6_MOUSE (10)
AP2M1_MOUSE (10)
ARI1A_MOUSE (10)
AT1A1_MOUSE (10)
AT2A2_MOUSE (10)
ATOX1_MOUSE (10)
ATPA_MOUSE (10)
ATPB_MOUSE (10)
ATPO_MOUSE (10)
BAF_MOUSE (10)
BCLF1_MOUSE (10)
BIP_MOUSE (10)
BOLA1_MOUSE (10)

ENSEMBL ID

ENSG00000170477 (34)
ENSG00000147251 (11)
ENSG00000247315 (7)
ENSG00000229353 (2)

CHEBI ID

CHEBI:30769 (4)
CHEBI:26271 (3)
CHEBI:18237 (3)
CHEBI:18186 (3)
CHEBI:26986 (3)
CHEBI:16811 (3)
CHEBI:24898 (3)
CHEBI:16610 (3)
CHEBI:6650 (3)
CHEBI:28044 (3)
CHEBI:16865 (3)
CHEBI:16235 (3)
CHEBI:16335 (3)
CHEBI:17568 (3)
CHEBI:15940 (3)
CHEBI:27266 (3)
CHEBI:30915 (3)
CHEBI:27897 (3)
CHEBI:167079 (2)
CHEBI:61724 (2)
CHEBI:15384 (2)
CHEBI:25351 (2)
CHEBI:17694 (2)
CHEBI:28846 (2)
CHEBI:67021 (2)
CHEBI:145277 (2)
CHEBI:17804 (2)
CHEBI:37270 (2)
CHEBI:28997 (2)
CHEBI:84323 (2)

Metabolite Name

Citric acid (4)
DCDP (2)
S-Lactoylglutathione (2)
DTDP (2)
LysoPC(18:1(11Z)) (2)
Phenylacetic acid (2)
Propionylcarnitine (2)
Glutathione (2)
4-Pyridoxic acid (2)
Kynurenic acid (2)
5-Hydroxyindoleacetic acid (2)
Malic acid (2)
4-Guanidinobutyric acid (2)
Tyrosine (2)
Glutamic acid (2)
Hypoxanthine (2)
DG(42:1) (1)
DG(44:12) (1)
DG(40:3) (1)
DG(44:4) (1)
DG(44:3) (1)
DG(40:1) (1)
DG(35:0) (1)
DG(35:2) (1)
DG(33:2) (1)
DG(42:5) (1)
DG(40:2) (1)
DG(28:0) (1)
DG(33:5) (1)
DG(41:3) (1)

First Public Date

2013 (13)
2014 (7)
2026 (6)
2025 (5)
2024 (5)
2020 (5)
2019 (5)
2015 (4)
2018 (3)
2017 (3)
2022 (1)
2021 (1)
2016 (1)

Classification

bacteria (5)
protozoa (1)

Modification

4x(15)N labeled L-arginine (51)
2x(15)N labeled L-lysine (49)
15.994915 (40)
4-tetrahydrothiazine-3-carboxylic acid (37)
57.021464 (36)
N6 (31)
Not available (28)
N6-dimethyl-L-lysine (26)
42.010565 (23)
-17.026549 (17)
4x(2)H labeled dimethylated residue (12)
4 (11)
-18.010565 (10)
+3amu) (7)
15.99491 (7)
57.02146 (7)
6x(2)H labeled dimethylated L-arginine (7)
79.966331 (6)
0.984016 (5)
45.029395 (5)
4x(2)H labeled dimethylated L-lysine (5)
58.005479 (4)
0.984 (3)
10.008269 (3)
3x(2)H labeled N6-acetyl-L-lysine (3)
42.01056 (2)
43.00581 (2)
Heavy form - site K (2)
-17.0266 (1)
-93.057849 (1)

Study type

RNA-seq of coding RNA (74)
Transcription profiling by array (15)
ChIP-seq (7)
High-throughput sequencing (2)
RNA-seq of total RNA (2)
RNA-seq of non coding RNA (2)
CLIP-Seq (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Proteomic profiling by mass spectrometer (1)
MicroRNA profiling by high throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
RIP-seq (1)
DNA-seq (1)
Proteomic profiling by array (1)

Release Date

2021 (117)
2022 (102)
2020 (94)
2019 (90)
2016 (81)
2023 (77)
2018 (75)
2015 (73)
2014 (73)
2025 (70)
2017 (63)
2013 (56)
2024 (54)
2012 (50)
2010 (41)
2011 (40)
2009 (31)
2026 (16)
2008 (15)
2007 (13)
2005 (6)
2006 (4)
2004 (1)
2002 (1)

Lab affiliation

University of Vienna, Faculty of Chemistry, Department of Analytical Chemistry (131)
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA., Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA (82)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (76)
EDyP (54)
CEA-Marcoule, ProGenoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Ceze, France (53)
Pacific Northwest National Laboratory (49)
Cellzome (42)
University of Victoria (38)
Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, OncoProteomics Laboratory, Amsterdam, Netherlands (36)
Wageningen University (36)
University Hospital Cologne (32)
Vanderbilt University (32)
Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg im Breisgau, Germany (28)
Head of the Curie Institute Mass Spectrometry Platform (28)
University of Edinburgh (28)
Head of Proteomics (27)
OncoProteomics Laboratory, Dept of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands (27)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (26)
The University of Melbourne (25)
Institute for Research in Immunology and Cancer, Department of Biochemistry, Department of Chemistry, Université de Montréal, Québec, Canada H3T 1J4 (22)
Institute of Molecular Biology (IMB) (22)
North Carolina State University (22)
Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital (22)
The University of Sydney (22)
European Molecular Biology Laboratory (21)
Cornell University (20)
Pacific Northwest National Laboratory, USA (20)
Proteomics facility, Central Science Laboratory, University of Tasmania (20)
University of Washington (20)
Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia (19)

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Shotgun lipidomics of HeLa whole-cell lysates and lysosomes following LLOMe treatment

Perturbations in lysosome integrity are tightly linked to neurological disorders and ageing, but the underlying pathogenic mechanisms are incompletely understood. Using an unbiased proteomic approach, we here identified the bridge-like lipid transport protein VPS13C/PARK23 as a key component of a...

2026-07-03 | MTBLS14737 | MetaboLights

LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets (Rat cardiomyocyte assay)

Lipids are dynamic constituents of biological systems, rapidly responding to any changes in physiological conditions. Thus, there is a large interest in lipid-derived markers for diagnostic and prognostic applications, especially in translational and systems medicine research. As lipid identificatio...

2018-07-31 | MTBLS483 | MetaboLights

Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation (Shotgun lipidomics assays without inhibition)

During megakaryopoiesis, megakaryocytes (MK) undergo cellular morphological changes with strong modification of membrane composition and lipid signaling. Here we adopt a lipid-centric multi-omics approach to create a quantitative map of the MK lipidome during maturation and proplatelet formation....

2023-07-26 | MTBLS6082 | MetaboLights

Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation (Shotgun lipidomics assays after inhibition with FSG67 and Triacsin C)

2023-07-26 | MTBLS6083 | MetaboLights

A label-free shotgun proteomics analysis of macadamia nut

In this study, we present a first proteomic overview of macadamia nut using a label-free shotgun proteomic approach and prediction of their proteins with potential allergenic activity and cross-reactivity via an in silico analysis. The defense response proteins were the most abundant group of protei...

ORGANISM(S): Macadamia

2020-01-13 | PXD015364 | Pride